Summary Statistics after dada2

User Support
#1

Hi,

I have done the analysis using QIIME2. I was wondering if there is a way where I can get information as done in the dada2 tutorial.

getN <- function(x) sum(getUniques(x))
track <- cbind(out, sapply(dadaFs, getN), sapply(dadaRs, getN), sapply(mergers, getN), rowSums(seqtab.nochim))

If processing a single sample, remove the sapply calls: e.g. replace sapply(dadaFs, getN) with getN(dadaFs)

colnames(track) <- c(“input”, “filtered”, “denoisedF”, “denoisedR”, “merged”, “nonchim”)
rownames(track) <- sample.names
head(track)

input filtered denoisedF denoisedR merged nonchim

F3D0 7793 7113 6976 6979 6540 6528

F3D1 5869 5299 5227 5239 5028 5017

F3D141 5958 5463 5331 5357 4986 4863

F3D142 3183 2914 2799 2830 2595 2521

F3D143 3178 2941 2822 2867 2552 2518

F3D144 4827 4312 4151 4228 3627 3488

Can we get the similar summary using QIIME2?

#2

Hi @shashankgpt,

That information is now stored in an artifact, if you look at this step of the moving pictures tutorial there’s a command qiime metadata tabulate which will render out the denoising-stats artifact.

This does require QIIME 2 2018.4 if I recall correctly.

#3

Hey!
Thanks for the information. QIIME 2 2018.4 does have this function, but I have done the analysis using QIIME 2 2018.2. Is there any other way where I can make it work using the current version of QIIME2 2018.2 or I have to update it?

Secondly, I used this command for denoise (QIIME 2 2018.2 version )-
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --o-table table --o-representative-sequences rep-seqs --p-trim-left-f 6 --p-trim-left-r 6 --p-trunc-len-f 270 --p-trunc-len-r 200 --p-n-threads 20 --verbose &> dada2.log

If I use the same command in QIIME 2 2018.4 version, do I get the same result?

Thanks

#5

Hey @shashankgpt,

You’ll need to update to 2018.4

Yes, there shouldn’t be any differences in DADA2’s denoised ASVs between 2018.2 and 2108.4, no defaults were changed and the same version is used.

#6

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.